Phenotypic and Genotypic Adaptation of Escherichia coli to Thermal Stress is Contingent on Genetic Background

Evolution can be contingent on history, but we do not yet have a clear understanding of the processes and dynamics that govern contingency. Here, we performed the second phase of a two-phase evolution experiment to investigate features of contingency. The first phase of the experiment was based on Escherichia coli clones that had evolved at the stressful temperature of 42.2 degrees C. The Phase 1 lines generally evolved through two adaptive pathways: mutations of rpoB, which encodes the beta subunit of RNA polymerase, or through rho, a transcriptional terminator. We hypothesized that epistatic interactions within the two pathways constrained their future adaptative potential, thus affecting patterns of historical contingency. Using ten different E. coli Founders representing both adaptive pathways, we performed a second phase of evolution at 19.0 degrees C to investigate how prior genetic divergence or adaptive pathway (rpoB vs. rho) affects evolutionary outcomes. We found that phenotype, as measured by relative fitness, was contingent on founder genotypes and pathways. This finding extended to genotypes, because E. coli from different Phase 1 histories evolved by adaptive mutations in distinct sets of genes. Our results suggest that evolution depends critically on genetic history, likely due to idiosyncratic epistatic interactions within and between evolutionary modules.

Automated summary

Evolution is influenced by historical contingency, however, the underlying processes and dynamics governing this contingency are not well understood. In this study, a two-phase evolution experiment was conducted to investigate the features of contingency. The first phase involved the evolution of Escherichia coli clones under stressful conditions, with two adaptive pathways identified: mutations in rpoB or rho genes. The second phase explored how genetic divergence and adaptive pathway affected evolutionary outcomes. The results showed that phenotype and genotype were contingent on founder genotypes and pathways, suggesting that evolution is heavily influenced by genetic history and idiosyncratic epistatic interactions.